RetrogeneDB ID: retro_ecab_1072

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:55514089..55514599(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000019315
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNBP
• Ensembl ID: ENSECAG00000009512
• Aliases: None
• Description: CCHC-type zinc finger, nucleic acid binding protein [Source:HGNC Symbol;Acc:13164]

Sequence

>retro_ecab_1072
ATGAGCAGTAAGGACTGCTTCAGGGGTGGACGCTCTGGCCACTGGGCCCGGGGATGCCCTAGAGGAGGAGCTCGAGGGCG
CGGAGCTAGAGGCCGTGGCAGAGGTTCTCAGGGCACTTCCACCACCCTACCTGACATCTGTTACCGCTGCGGTGAGTCTG
GTCATCATGCTAGGGACTGTCACCTTCTCGAGAACATCTGCTACAACTGTGGGAGAAGTGGCCACATTGCCAAAGACTGT
ACGGAGCCTAAGCGAGAGAGGGAGCAGTGCTGTTACACTTGTGGCAGACGAGGCCATCTGGCTCGCGATTGTGACCGTCA
GGAACAGCAAAAGTGTTACTCTTGCGGCGAATTAGGCCACTTTCAGAAAGACTGTACCCAAGTCAAGTGCTACCGGTGTG
GCGAGACCGGCCACGTGGCCATCAACTGTAGCAAGAAGAACAAGGTCAATTGCTACCGCTGTGGCAAGCCCGGACATCTA
GCCCGGGAATGCCCCACTGAGGCTACCGCT

Alignment

ORF - retro_ecab_1072 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGFQFVSSSLPDICYRCGESGHLAKDCDLQEDACYNC
          MSS..CF..GRSGHWAR.CP.GG.RGRG.R.RGRG.Q..S..LPDICYRCGESGH.A.DC.L.E..CYNC
Retrocopy MSSKDCFRGGRSGHWARGCPRGGARGRGARGRGRGSQGTSTTLPDICYRCGESGHHARDCHLLENICYNC

Parental  GRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVA
          GR.GHIAKDC.EPKREREQCCY.CG..GHLARDCD....QKCYSCGE.GH.QKDCT.VKCYRCGETGHVA
Retrocopy GRSGHIAKDCTEPKREREQCCYTCGRRGHLARDCDRQEQQKCYSCGELGHFQKDCTQVKCYRCGETGHVA

Parental  INCSKTSEVNCYRCGESGHLARECTIEATA
          INCSK...VNCYRCG..GHLAREC..EATA
Retrocopy INCSKKNKVNCYRCGKPGHLARECPTEATA

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	0.00 RPM	192.26 RPM
SRP021940_cerebellum	0.00 RPM	176.15 RPM
SRP021940_embryo	0.05 RPM	153.79 RPM
SRP021940_placental_villous	0.10 RPM	126.29 RPM
SRP021940_synovial_membrane	0.00 RPM	118.62 RPM
SRP021940_testis	9.91 RPM	152.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1072 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1072 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_50
Pongo abelii	retro_pabe_3658

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012159	1 retrocopy	retro_btau_19,
Callithrix jacchus	ENSCJAG00000017430	1 retrocopy	retro_cjac_4079,
Equus caballus	ENSECAG00000009512	1 retrocopy	retro_ecab_1072 ,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Loxodonta africana	ENSLAFG00000002502	1 retrocopy	retro_lafr_49,
Oryctolagus cuniculus	ENSOCUG00000008696	2 retrocopies	retro_ocun_1626, retro_ocun_208,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Pteropus vampyrus	ENSPVAG00000015070	1 retrocopy	retro_pvam_908,
Sorex araneus	ENSSARG00000011874	1 retrocopy	retro_sara_397,
Sarcophilus harrisii	ENSSHAG00000017132	1 retrocopy	retro_shar_666,