RetrogeneDB ID: retro_tbel_1335

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4421:78..946(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000017170
• Aliases: None
• Description: None

Sequence

>retro_tbel_1335
ATGGGAAAGAAGGAGTCTCACATCAACATTGTTGTCATTGGACACGTAGATTCCTGCAAGTCCACAACTACTGGCCATCT
GATCGACAAATGTGGTGGGATCAACAAAAGAACCATCAGAAAATTTGAGAAGGAGGCTGCTGAGATGGGAAAGGGCTCCT
TCAAATACGCCTGGGTCTTGAATAAACTGAAAGCTGAACGTGAGCATGGTATCACCACTGATATCTCCCTGTGGAAGTTT
GAGACCAGCAAGTATTATGTGACTATCATCGATGCCCCAGGACACAGAGACATTATCCAAAACATGATTACAGACGCATC
TCAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTAGTGAATTTGAAGCTGGTATCTCCAAGAACGGGCAGACCT
GTGAGCATGCCCTTCTGGCTTACACACTGGGTGTGAAACAACTAATTGTTGGTGTTAACAAAATGAATTCTACTGAGCCA
CCCTACAGTCAGAAGAGATATGAGGAAATTGTTAAAGAAGTCAGCACCTACATTAAGAAAATTGGTTACAATCCTGATGT
GGTAGCATTTGTGCCAGTTTCTGGTTGGAATGGTGACAACATGTTGGAGCCAAGTGCTAATATGCCATAGTTCATGGGGT
ATTAAAGTCACCCATAAAGATGGCAATGCCAGTGGAACCACACTGCTTGAAGCTCTGGATTGCATCCTACTACCAACTCG
TCCAACTGACAAGCCCTTGCATCTGCCCCTCTAGGATGTGTACACTATCGGTGGTATTGGCACTGTCCCCGTGGGCCGAG
TGGAGACTGGTGTGCTCAAACCTGGTATGGTGGTCACCTTTGCACCAGTGAATGTGACAACTGAAGTA

Alignment

ORF - retro_tbel_1335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.7 %
• Parental protein coverage: 82.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHTNIVVIEHVDSGKSTTSGHLIDKCGGVDQRIMEKIEKEAAEMGKGSFKDVWVLDKQKA--EHG
          MGK...H.NIVVI.HVDS.KSTT.GHLIDKCGG...R...K.EKEAAEMGKGSFK..WVL.K.KA..EHG
Retrocopy MGKKESHINIVVIGHVDSCKSTTTGHLIDKCGGINKRTIRKFEKEAAEMGKGSFKYAWVLNKLKAEREHG

Parental  TTIGISLWKSETSK-FVTIID--GHRDFIKNMIT--GTANCAVPIAAAAVGEPEAGIPKNGQTREHALLV
          .T..ISLWK.ETSK..VTIID..GHRD.I.NMIT....A.CAV.I.AA.V.E.EAGI.KNGQT.EHALL.
Retrocopy ITTDISLWKFETSKYYVTIIDAPGHRDIIQNMITDASQADCAVLIVAAGVSEFEAGISKNGQTCEHALLA

Parental  YTLGVKQLMVGVNKMDSTESPYSQKRYKEIV--VSTYIKKVSTYNLDTVVYVSISGWNGDNMLHPSANMP
          YTLGVKQL.VGVNKM.STE.PYSQKRY.EIV..VSTYIKK...YN.D.V..V..SGWNGDNML.PSANMP
Retrocopy YTLGVKQLIVGVNKMNSTEPPYSQKRYEEIVKEVSTYIKKIG-YNPDVVAFVPVSGWNGDNMLEPSANMP

Parental  WFIGW-KVTHKGGSANESKLHETLDRILALTYTTDKSLYLPV-ELYKICGIGTVSVSQLESGILKPGIVV
          .F.G..KVTHK.G.A....L.E.LD.IL..T..TDK.L.LP....Y.I.GIGTV.V...E.G.LKPG.VV
Retrocopy *FMGY>KVTHKDGNASGTTLLEALDCILLPTRPTDKPLHLPL*DVYTIGGIGTVPVGRVETGVLKPGMVV

Parental  TFAPINVITEI
          TFAP.NV.TE.
Retrocopy TFAPVNVTTEV

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_1335 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1335 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Tupaia belangeri	ENSTBEG00000012151	51 retrocopies	retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354, retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125, retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Tupaia belangeri	ENSTBEG00000017170	16 retrocopies	retro_tbel_1335 , retro_tbel_1406, retro_tbel_2677, retro_tbel_2899, retro_tbel_2966, retro_tbel_3336, retro_tbel_348, retro_tbel_3485, retro_tbel_3658, retro_tbel_3727, retro_tbel_3948, retro_tbel_4091, retro_tbel_4127, retro_tbel_4290, retro_tbel_4507, retro_tbel_4527,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,