RetrogeneDB ID: retro_ecab_810

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:50306245..50307660(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000018100
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000017343
• Aliases: None
• Description: None

Sequence

>retro_ecab_810
ATGGTGGCAGGCAAAGTTGCAATGGCTATGGGGCAGCCGCATCTTTCTCGCCAGGGTCTGGCCAACTTGGATGTTACCAA
GTTGACTCCTCTCTCTCACAAAGTTATCAGCAGACAAGCCACAATTAACATAGGTACAATTGGTCATGTTGCTCATGGAA
AATCTACAGTTGTAAAAGCTATTTCTGGAGTTCACACTGTCAGGTTCAAAAATGAACTGGAAAGAAATACTACAATCAAG
CTTGGATATGTGAATGCCAAGATTTATAAACTTAATGATGCAAGTTCTCCTCGACCAGAATGCTACAGATCCTGTGGAAG
CAGTACACCTGATGAATTTCCTTCAGACATTCCAGGGACCAGAAGGAACTTTAGACTTGTCAGACATGTTTCCTTTGTTG
ACTGTCCTGGCCATGATATTTTGATGGCTATTATGCTGAATGGTGCAACAGTGATGGATGCAGCTCTTTGGTTGATAGCT
GGTAATGAATCTTGTCCTCAACCTCAGACTTCTGAACACCTGGCTGCCATAGAAATTATGAAGCTGAAACATATTTTGAT
TCTACAGAATAAAATTGATTTGGTAAAAGAAAGTCAGGCTAAAGAACAGTATGAACAGATCCTTGCATTTGTACAAGGTA
CAGTAGAAGAAGCAGCTCCCATTATTCCAATTTCTGTACAGCTGAAATATAATATTGAAGTTGTCTGTGAGTATATTGCA
AAGAAAATTCCAGTACCTCTAAGAGACTTTACGTCAGAACCCCAACTTATTGTTATTAGGTACTTTGCTGTCAACAAACC
TGGCTGTGAGGTTGATGACCTTAAAGGTGGTAGGGCTGGTGGTAGTATTTTAAAAGGAGTTTAAAGGTGGGCCAGGAGAT
AGAAGTCAGACCTGATATTGTTTCCAAAGATAGTGAAGGAAAACTCATGTGTAAACCAATCTTTTCCAAAATTGTATCAC
TTTTTGCAGAACATAATGATCTTCAGTATGCTGCTCCACGGGGTCTTATTGGAGTTGGAACAAAAAGTGACCCCACTTTG
TGCCGGGCTGATAGGATGGTGGGGCAGGTACTTGGTGCAGTTGGAGCTTTACCAGAGATCTTCACAGAATTGGAAATTTC
CTATTTCCTACTTAGACGGCTCCTTGGTGTACGGACAGAGGAAGACAAAAAAGCAGCAAAGGTGCAAAAGCTGTCTAAGA
ATGAAGTGCTTATGGTGAACACAGGATCCTTGTCAACAGAAGGAAGAGTGAGTGCAGTTAAGGCTGACTTGGGTAAAACG
GTTCTCACTAATCCTGAATGCACGGAAGTAGGAGAAAAAATTGCCCTCAGCCAAAGAGTTGAGAAACACTGGTGTTTAAT
TGGTTGGGGTCAGATAAGAAGAGGAGTAACCATCAAGGCAACAGTAGCTGATGAC

Alignment

ORF - retro_ecab_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGGEAGVTLGQPHLSRQDLATLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFK
          M..G......GQPHLSRQ.LA.LDVTKLTPLSH.VISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFK
Retrocopy MVAGKVAMAMGQPHLSRQGLANLDVTKLTPLSHKVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFK

Parental  NELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFRLVRHVSFVDCPGHDI
          NELERN.TIKLGY.NAKIYKL.D.S.PRPECYRSCGSSTPDEFP.DIPGT..NFRLVRHVSFVDCPGHDI
Retrocopy NELERNTTIKLGYVNAKIYKLNDASSPRPECYRSCGSSTPDEFPSDIPGTRRNFRLVRHVSFVDCPGHDI

Parental  LMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAF
          LMA.MLNGA.VMDAAL.LIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAF
Retrocopy LMAIMLNGATVMDAALWLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAF

Parental  VQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAG
          VQGTV.E.APIIPIS.QLKYNIEVVCEYI.KKIPVP.RDFTSEP.LIVIR.F.VNKPGCEVDDLKGG.AG
Retrocopy VQGTVEEAAPIIPISVQLKYNIEVVCEYIAKKIPVPLRDFTSEPQLIVIRYFAVNKPGCEVDDLKGGRAG

Parental  GSILKGV-LKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCR
          GSILKGV.LKVGQEIEVRP.IVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAP.GLIGVGTK.DPTLCR
Retrocopy GSILKGV<LKVGQEIEVRPDIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPRGLIGVGTKSDPTLCR

Parental  ADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSA
          ADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTE.DKKAAKVQKLSKNEVLMVN.GSLST.GRVSA
Retrocopy ADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEEDKKAAKVQKLSKNEVLMVNTGSLSTEGRVSA

Parental  VKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD
          VKADLGK.VLTNP.CTEVGEKIALS.RVEKHW.LIGWGQIRRGVTIK.TV.DD
Retrocopy VKADLGKTVLTNPECTEVGEKIALSQRVEKHWCLIGWGQIRRGVTIKATVADD

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
SRP021940_articular_cartilage	3.84 RPM	46.16 RPM
SRP021940_cerebellum	0.00 RPM	28.82 RPM
SRP021940_embryo	11.56 RPM	70.15 RPM
SRP021940_placental_villous	0.00 RPM	67.98 RPM
SRP021940_synovial_membrane	3.95 RPM	39.01 RPM
SRP021940_testis	1.79 RPM	7.35 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_810 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_810 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_810 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810 ,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Mus musculus	ENSMUSG00000035150	2 retrocopies	retro_mmus_1408, retro_mmus_3433,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,