RetrogeneDB ID: retro_ecab_17

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un0608:6503..7487(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004011
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000009507
• Aliases: None
• Description: None

Sequence

>retro_ecab_17
ATGAGTTTTCTTGGAGGCTCTTTTGGTCCCATTTGTGAGGTCGATGTTGTCCTTAATGATGGGGAAACCAGGAAAATGGC
AGAAATGAAAACTGAAGATGGCAAAGTAGAAAAACACTATCTTTTCTATGATGGAGAATCTGTTTCGGGAAAGGTAAACC
TAGCCTTTAAGCAACCTGGAAAGAGGCTAGAGCACCAAGGAATTAGAATTGAATTTGTAGGTCAAATTGAACTTTTCAAT
GACAAGAGTAATACTCACGAATTTGTAAACCTAGTGAAAGAACTGGCCTTACCTGGAGAACTGACTCAGAGCAGAAGTTA
TGATTTTGAATTTATGCAAGTTGAAAAGCCATATGAATCTTACATCGGTGCCAATGTCCGCTTGAGGTATTTTCTTAAAG
TGACAATAGTAAGAAGACTGACAGACTTGGTAAAAGAATATGATCTTATTGTTCACCAGCTTGCCACCTATCCTGATGTT
AACAACTCTATTAAGATGGAAGTGGGCATTGAAGATTGTCTACATATAGAATTTGAATATAATAAATCAAAGTATCATTT
AAAGGATGTGATTGTTGGAAAAATTTACTTCTTATTAGTAAGAATAAAAATCCAACATATGGAGTTACAGCTGATCAAAA
AAGAGATCACAGGAATTGGACCCAGTACCACAACAGAAACGGAAACAATTGCTAAATATGAAATAATGGATGGTGCACCA
GTAAAAGGTGAATCAATTCCAATACGACTATTTTTAGCAGGATATGACCCAACTCCAACAATGAGAGATGTGAACAAAAA
ATTTTCCGTAAGGTACTTTTTGAATCTAGTCCTTGTTGATGAGGAAGACAGAAGGTACTTCAAGCAGCAGGAAATCATTT
TATGGAGAAAAGCTCCTGAAAAACTGAGGAAACAGAGAACAAACTTTCACCAGCGATTTGAATCTCCAGAATCACAGGCA
TCTGCTGAACAGCCTGAAATGTGA

Alignment

ORF - retro_ecab_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.08 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFLGGFFGPICEIDVVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIE
          SFLGG.FGPICE.DVVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIE
Retrocopy SFLGGSFGPICEVDVVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIE

Parental  FVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRLT
          FVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRLT
Retrocopy FVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRLT

Parental  DLVK-YDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQL
          DLVK.YDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQL
Retrocopy DLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQL

Parental  IKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDE
          IKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDE
Retrocopy IKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDE

Parental  EDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM
          EDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM
Retrocopy EDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEM

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	0.35 RPM	1.12 RPM
SRP021940_cerebellum	0.42 RPM	1.09 RPM
SRP021940_embryo	0.54 RPM	1.71 RPM
SRP021940_placental_villous	0.72 RPM	2.17 RPM
SRP021940_synovial_membrane	0.41 RPM	1.40 RPM
SRP021940_testis	1.53 RPM	5.50 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_17 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_17 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_17 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013827	1 retrocopy	retro_cfam_1133,
Choloepus hoffmanni	ENSCHOG00000007324	5 retrocopies	retro_chof_1303, retro_chof_1663, retro_chof_1796, retro_chof_2352, retro_chof_242,
Callithrix jacchus	ENSCJAG00000012907	1 retrocopy	retro_cjac_1420,
Equus caballus	ENSECAG00000009507	1 retrocopy	retro_ecab_17 ,
Homo sapiens	ENSG00000122958	1 retrocopy	retro_hsap_2688,
Gorilla gorilla	ENSGGOG00000010433	1 retrocopy	retro_ggor_1875,
Microcebus murinus	ENSMICG00000014940	1 retrocopy	retro_mmur_1070,
Mustela putorius furo	ENSMPUG00000004519	1 retrocopy	retro_mputfur_146,
Nomascus leucogenys	ENSNLEG00000011548	1 retrocopy	retro_nleu_1187,
Pongo abelii	ENSPPYG00000002386	1 retrocopy	retro_pabe_2293,
Pan troglodytes	ENSPTRG00000002567	3 retrocopies	retro_ptro_1815, retro_ptro_2245, retro_ptro_4,
Tupaia belangeri	ENSTBEG00000015348	1 retrocopy	retro_tbel_1425,
Vicugna pacos	ENSVPAG00000000630	1 retrocopy	retro_vpac_385,