RetrogeneDB ID: retro_ecab_988

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:26013034..26013363(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FGFR1OP2
• Ensembl ID: ENSECAG00000016890
• Aliases: None
• Description: FGFR1 oncogene partner 2 [Source:HGNC Symbol;Acc:23098]

Sequence

>retro_ecab_988
AAAATGAATTGCACAATTGAGAGAGCATTGGTCGATGCTAAAGTTCTCATTGAAAGATTGGGAGATTATGACAGTGCAGC
AGAATCTCGTACTGAGCAAACTGTACCTCTCACCCAGCACGCAGAAGCCATCAAGTAGCATCAGGAAAAAACCCAGAATC
TAATGACTTTGCATGTCCACCATGGCCTACGTTAATTAAGGGCATCCAGCAAGAAAACTGACAGATCAGAGCACTGCAAT
ATGACAACAAATAATTCCGTACATCCTGGGAGAAACACCAGTGAGCGCTGGGACTTAGAATGAACAAGTACCAAGAGCAA
ATATTTAGG

Alignment

ORF - retro_ecab_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.04 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EMSCTIEKALADAKALVERLRDHDDAAESLIEQTTALNKRVEAMKQYQEEIQ-ELNEVARHRPRSTLVMG
          .M.CTIE.AL.DAK.L.ERL.D.D.AAES..EQT..L....EA.K..QE..Q.E.N..A...P..TL..G
Retrocopy KMNCTIERALVDAKVLIERLGDYDSAAESRTEQTVPLTQHAEAIK*HQEKTQ<ESNDFACP-PWPTLIKG

Parental  IQQENRQIRELQQENK-LRTSLEEHQSALELIMSKYREQMFR
          IQQEN.QIR.LQ..NK..RTS.E.HQ.AL.L.M.KY.EQ.FR
Retrocopy IQQEN*QIRALQYDNK*FRTSWEKHQ*ALGLRMNKYQEQIFR

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	5.37 RPM
SRP021940_cerebellum	0.00 RPM	4.05 RPM
SRP021940_embryo	0.00 RPM	7.67 RPM
SRP021940_placental_villous	0.00 RPM	4.62 RPM
SRP021940_synovial_membrane	0.00 RPM	5.66 RPM
SRP021940_testis	0.00 RPM	3.77 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_988 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_988 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988 ,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608,