RetrogeneDB ID: retro_acar_15

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:45808435..45812098(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000012451
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSACAG00000013791
• Aliases: None
• Description: None

Sequence

>retro_acar_15
ATGGCTCTATTGTTTACAGGACATTCCTTATTTTTAGCATTAGCAATGTTGGCAGTCTGCACTTTTGAAGAGTCGGTGAG
TAATTACTCAGATTGGGTGACTTTTACAGAGAATGTGGATCAGTATGAGAAACAGAGACTGGAAGATTTCAAGGCTGATC
AGAAGATGAAAAGAACCATCCCTCATCCAAGCTTGTATTTCAGTGCTGAAGAAGTCCCAGCATTGAGGCAGAAATCTCAC
ACCAGCCATCTCCACCTCTTTAGAGCAATCAGGAGTGCAGTGTCTGTGATGCTCTCCAATCCATCCTACTACCTACCTCC
ACTCAAGCATGCCGATTTTGCTGCAAAGTGGAATGAGATCTATGGAAACAATTTGCCTCCCTTAGCATTTTACTGTCTCC
TGTGTCCAGAAGATAAAGCTGCCTTTGAATTTGTTTTGGAATATATGGACAGGTTGGCTGGATACAAAGACTGGCTGGTA
GAGAATGCCCCGGGTGATGAGGTTCCTCTTGGGCATTCCTTAACAGGCTTTGCCACAGCGTTTGATTTTCTGTATTCCAC
CCTGGATGATGACAGAAGGCAAAACTACTTAGCCAAGATCTTGGCTGTGAGCGAGGAAATGTATGAATATTCCAAAGTCC
GTTCCTGGGGCAAGCAACTACTTCACAACCACCAAGCCACTAACATGGTGGCATTGCTCATTGGGGCTTTGGTAACCGAA
GGGGGCATAGAGGCCCAAGCTAACATCTGGAAGCATACAGTAGTGGATGTGATGGAAAAAACCATGTTTTTGCTAAACCA
TATTGTGGATGGCTCTTTGGATGAAGGTGTAGCATATGGCAGCTATACATCCAAATCCATCACCCAGTATATTTTTCTGG
CACAGCGCCACTTTGGGATTAACAATTTTGAAAACCACTGGCTCAAAATGCACTTTTGGTTTTATTATGCTACCCTTTTG
CCTGGCTTTCAGAGAACTGTGGGCATAGCTGATTCTAATTACAATTGGTTTTATGGACCTGAAAGCCAGCTGGTTTTCCT
TGACAGGTTTGTGCTGAAGAATGGCATAGGCAATTGGCTTGCACAGCAAATTAGAAAGCACCGCCCAAAAGATGGCCCTA
TGGTACCATCCACTGCTCAAAGATGGAGTACACTTCACACAGAGTACTTATGGTATGACCCAGGATTAACGCCTCATCCT
CCTCCTGACTATGGCAGTGCGAAAATGCATGTGTTCCCTAACTGGGGTGTTGTTACCTATGGGGCAGGGTTACCATATGG
ACAGACAAATACCTTTGTTTCTTTCAAATCTGGAAAGCTGGGTGGCCGTGCTGTCTATGACATAGTCCACTTTCAGCCAT
ATTCCTGGATTGATGGTTGGCGGAGTTTCAACCCAGGGCATGAACACCCCGATCAGAACTCTTTCACCTTTGCTCCCAAT
GGACAAGTGTTTGTCTCCGAGGCCCTGTATGGCCCCAAACTCAGCCACCTGAATAATGTCCTGGTGTTTGCACCATCTCC
AACAAGTCAGTGCAATCAGCCTTGGGAGGGTCAACTTGGGGAGTGCACACAGTGGCTAAAGTGGACAGGGGATGAAGTTG
GAGATGCTGCTGGTGAGATAATAACATCCTCTCAGCACGAGGACATGATGTTTGTGAGTGGCGAGGCAGCATCCACATAT
TCCTCAGCTATGAAGCTCAAAAGTGTCTACCGTTCATTACTTCTGTTGAATCACCAGACTCTGCTAGTGGTTGACCATGT
GGAAAAGGAGGTGGACTCTCCCATCAACTCCATCAGTGCCTTTTTTCATAACCTTGACATTGACTTTAAATATGTCCCCT
ATAAATTTATGAACAAATATAATGGAGCCATGATGGATGTATGGGATGCTCACTATAAAATGTTTTGGTTTGACCATCAT
GGCAGCAGTCCTGTTGCTAGGATACAAGAGGCAGAGCAGGCAGCCGAGTTCAAAAAGAGGTGGACGCAGTTTGTAAATGT
CACTTTTTCTGCAAAAAGTACTACTGCAAGAATTGCCTATGTGTTCTATGGGCCTTATGTCAACGTTTCAAGCTGTAGAT
TTGTTGATGATGCCCAAGCAGGGTTTCGAATATCTTTGAATGTCAACAATACTGAAACTGTTTTCTCAGTTGTCACAGAC
TATCTAAACCTGGGGACAAGGTTCAATTATTTAGGTTTTGGTGGCTATGCCAAGGTAACTACACAAGGAAAAGTTACAAG
ATTTGGTCTGGGTACAGAAGCAGTCAAAAAGCAGGCACTGAATAACAAGACTGTTTTCCCCTTTGGTTTTAAAGTGAATA
TAATAGCAGGACTGATTTTGGGGATTAGTTTGGTCATATTGGCCATCCAGTGGAGGTTTTACATATCTTTTGGCAAGCTT
TTGCGTTGGACCCTAATCTTGGTAATTCTGCTATGGTTTGTGGAACTGATTGATGTGTGGAGCTCTTGTACTCAACCAAT
CTGTGCAAAATGGAGTAGTGATGTAGCAAGTACAGAAGGCAATGCAGAGAAGGACCAAGGGCACCCTGTGACTTTGCCAG
ACATTGTCATTACTTCTCTCCCCAATTCAGGTGCAGAAATCTTGAAGCAACTGTTCTTCAACAGCAGTGACTTCATCTAC
ATTAGGATCCCTACAGGGTACCTTGATGTCCCCGAAACTGAATTTGAGATTGACTCATTTGTTGATGCCTGTGAATGGAA
AGCATCCGATGTTCAAAGTGGCCATTTTCGGCTCCTCCAGGGCTGGCTGCATTCTCTAGTCAAAGACACTAAGCTGCATT
TGCAAAATATTCATCTACATGAACCCAGCAGAAGTAAGTCGGCTCAGCATCCTTCCCCCAGCAAAGACAAAAAGAGGCGG
CCTAGAAAGAGAGAATCCATAGCAGAACAAAGAACCCGACTGAGAGGGAGTTCAGACAAAGAGGCTGAATACATTAGAGA
TCTGAGGAGACACCTTGCTTTTTATCCCAACGCACGCCCTGTGCTTAGTCTGAGCAGTGGGAGCTGGACATTAAAGCTGC
CTTTCTTTCAAGAAATCATAGGCCTTTCGCTGAGAGCACTCTATGTAGTCCGTGACCCTCGTGCATGGGTCCATTCAATA
CTATACAAAAGCCAGCCAAGCCTCTACTCATTGAGGAAGGTTCCTCAGCGTTTAGCTAGGCTATTTAAACCAGATGGCAA
GAGGAAAGACAAGTGTCATTTAAATTCAGGCTATGCCCTTGAATATGAGCCACTGAGGGAGGAACTTTCCCATTCAAATT
CAAACGCTGTCTCTGTGATGTCCCATTTGTGGCTGGCAAATACAGCAGCAGCCCTGAGGCTCAACGGGGATTTGCTGCCA
GCAAATTATCGCCTCCTCAAGTTTGAAGACATTGTCAACTTTCCCCATAAGGTGGCTGAAGCCGTCTATGCCTTTCTTGG
CATCCCTCTGTCTCCTGCTAGCTTAAACCAAATATTATTTGCCACATCCACCAATCTTTTTTATCTTCCTTATGAAGGGG
AGGTCTCTCCAGTGAGCATCCATGCTTGGCGACATGATCTGCCTCTGGAGGAAATTAAGCTGATCGAGGACATCTGTTCC
ACTCTAATGGACCGCTTAGGATATCCAAAGTTTACTGATTTAGATGCTGCGGGTCAGCAGTAG

Alignment

ORF - retro_acar_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.56 %
• Parental protein coverage: 66.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPMLYFSREDIPDLQTKATTTHQHIAVRLVEAVQIMLSNPLEYLPPWDPKDFSARWNEIYGNNLGALAMF
          .P.LYFS.E..P.L..K..T.H.H.......AV..MLSNP..YLPP....DF.A.WNEIYGNNL..LA..
Retrocopy HPSLYFSAEEVPALRQKSHTSHLHLFRAIRSAVSVMLSNPSYYLPPLKHADFAAKWNEIYGNNLPPLAFY

Parental  CLLYPENIEAVDMAKDYMERMAAQPSWLVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKSQQERFLEVIA
          CLL.PE...A......YM.R.A....WLV..AP.DEVPL.HSL.GFATA.DFLY..L........L..I.
Retrocopy CLLCPEDKAAFEFVLEYMDRLAGYKDWLVENAPGDEVPLGHSLTGFATAFDFLYSTLDDDRRQNYLAKIL

Parental  NASGYMYEASYRRGWGFQYLHNHQPTNCVALLAGSLILMNQGYLQEAYLWTKQVLAIMEKSIVLLQEVTD
          ..S..MYE.S..R.WG.Q.LHNHQ.TN.VALL.G.L.....G....A..W...V...MEK...LL....D
Retrocopy AVSEEMYEYSKVRSWGKQLLHNHQATNMVALLIGALVTEG-GIEAQANIWKHTVVDVMEKTMFLLNHIVD

Parental  GSLYEGVAYGSYTTRSLFQYIFLVQRHFDINHFNHPWLKQHFAFMYRTVLPGFQRTVAIADSNYNWFYGP
          GSL.EGVAYGSYT..S..QYIFL.QRHF.IN.F...WLK.HF.F.Y.T.LPGFQRTV.IADSNYNWFYGP
Retrocopy GSLDEGVAYGSYTSKSITQYIFLAQRHFGINNFENHWLKMHFWFYYATLLPGFQRTVGIADSNYNWFYGP

Parental  ESQLVFLDKFIMRNGSGNWLADQIRRNRVLEGPGTPSKGQRWCTLHTEFIWYDASLGFVPPPDYGIPKLH
          ESQLVFLD.F...NG.GNWLA.QIR..R...GP..PS..QRW.TLHTE..WYD..L...PPPDYG..K.H
Retrocopy ESQLVFLDRFVLKNGIGNWLAQQIRKHRPKDGPMVPSTAQRWSTLHTEYLWYDPGLTPHPPPDYGSAKMH

Parental  YFEDWGVVTYGSALPAEINRPFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAP
          .F..WGVVTYG..LP......F.SFKSGKLGGRA.YDIVH...Y..WI.GWR.FN.GHEHPDQNSFTFAP
Retrocopy VFPNWGVVTYGAGLPYGQTNTFVSFKSGKLGGRAVYDIVHFQPY-SWIDGWRSFNPGHEHPDQNSFTFAP

Parental  NGVPFITEALYGPKYTFLNNVLMFSPAVSKSCFYPWEGQVTEDCSSKWLKYKHDLAADCQGRVVAAMERS
          NG..F..EALYGPK...LNNVL.F.P.....C..PWEGQ..E.....WLK...D...D..G.........
Retrocopy NGQVFVSEALYGPKLSHLNNVLVFAPSPTSQCNQPWEGQLGE--CTQWLKWTGDEVGDAAGEIITSSQHE

Parental  GIIFIRGEGVGAYNPKLKLKSLQRNLFLIHPQLLLLVDQIHLADDSPLEMATSFFHNVDVPFEET---VI
          ...F..GE....Y....KLKS..R.L.L...Q.LL.VD......DSP......FFHN.D..F........
Retrocopy DMMFVSGEAASTYSSAMKLKSVYRSLLLLNHQTLLVVDHVEKEVDSPINSISAFFHNLDIDFKYVPYKFM

Parental  DNVHGAFIRQQDGLYKMYWMDDTGYSEKAVVTSRMYPRGYPYNGTNYVNVTTHLRKPVTSAVYLFIGPSV
          ....GA.....D..YKM.W.D..G.S..A...............T..VNVT...........Y.F.GP.V
Retrocopy NKYNGAMMDVWDAHYKMFWFDHHGSSPVARIQEAEQAAEFKKRWTQFVNVTFSAKSTTARIAYVFYGPYV

Parental  DVQSFSVHGDAQ
          .V.S.....DAQ
Retrocopy NVSSCRFVDDAQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP009831_adrenal	13.29 RPM	82.91 RPM
SRP009831_brain	69.68 RPM	10.46 RPM
SRP009831_dewlap	32.02 RPM	4.77 RPM
SRP009831_embryo	26.41 RPM	107.14 RPM
SRP009831_heart	14.89 RPM	16.24 RPM
SRP009831_liver	6.71 RPM	12.31 RPM
SRP009831_lung	13.05 RPM	38.54 RPM
SRP009831_ovary	33.47 RPM	2.16 RPM
SRP009831_skeletal_muscle	2.08 RPM	5.54 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_15 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_15 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15 ,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8,