RetrogeneDB ID: retro_ecab_62

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:81739381..81740221(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002732
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MORF4L1
• Ensembl ID: ENSECAG00000008091
• Aliases: None
• Description: mortality factor 4 like 1 [Source:HGNC Symbol;Acc:16989]

Sequence

>retro_ecab_62
NCTCGTGGACAACAATCTGCAGAAGAAGACAACTTCAAAAAACCAACTAGAAGCAATATGCAGAGAAGTAAGATGAGAGG
GGCCTCCTCAGGAAAGAAGACAGCTGGTCCACAGCAGAAGAATCTGGAACCGGCTCTCCCTGGCAGGTGGGGGGGTCGCT
CTGCGGAGAACCCGCCTTCAGGATCTGTGAGGAAGACAAGAAAGAACAAACAGAAGACTCCTGGAAACGGAGATGGTGGC
AGTACCAGCGAAGCACCTCAGCCACCTCGGAAGAAAAGGGCCCGGGCAGACCCCACCGTTGAAAGTGAAGAGGTGTTTAA
GAATAGAATGGAAGTTAAAGTGAAGATTCCTGAAGAATTAAAACCATGGCTTGTCGAGGACTGGGACTTAGTTACCAGGC
AGAAGCAGCTGTTTCAACTCCCTGCTAAGAAAAATGTAGATGCCATTCTGGAAGAGTATGCAGATTGCAAGAAGTCGCAG
GGAAATGTCGATAATAAGGAATATGCGGTTAATGAAGTCGTGGCAGGAATAAAAGAATATTTCAACGTGATGTTGGGCAC
TCAGCTGCTCTACAAATTTGAGAGGCCCCAGTATGCTGAAATCCTCTTGGCTCACCCTGATGCGCCGATGTCCCAGGTTT
ATGGAGCGCCACACCTACTGAGATTATTCGTAAGAATCGGAGCAATGTTGGCATATACGCCCCTTGATGAGAAGAGCCTT
GCATTATTGTTGGGCTATTTGCATGATTTCCTAAAATATCTGGCAAAGAATGCTGCGTCTCTGTTTACTGCCAGTGATTA
CAAGGTGGCTTCGGCTGAGTACCACCGCAAAGCCCTGTGA

Alignment

ORF - retro_ecab_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.84 %
• Parental protein coverage: 77.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRARVDPTVENEETF
          Q....E....G...G..........V..KT.KNKQKTPGNGDGGSTSE.PQPPRKKRAR.DPTVE.EE.F
Retrocopy QQKNLEPALPGRWGGRSAENPPSGSVR-KTRKNKQKTPGNGDGGSTSEAPQPPRKKRARADPTVESEEVF

Parental  MNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAG
          .NR.EVKVKIPEELKPWLV.DWDL.TRQKQLF.LPAKKNVD.ILE.YA..KKS.GN.DNKEYAVNEVVAG
Retrocopy KNRMEVKVKIPEELKPWLVEDWDLVTRQKQLFQLPAKKNVDAILEEYADCKKSQGNVDNKEYAVNEVVAG

Parental  IKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNY
          IKEYFNVMLGTQLLYKFERPQYAEIL..HPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLL.Y
Retrocopy IKEYFNVMLGTQLLYKFERPQYAEILLAHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLGY

Parental  LHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
          LHDFLKYLAKN.A.LF.ASDY.VA..EYHRKA.
Retrocopy LHDFLKYLAKNAASLFTASDYKVASAEYHRKAL

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	60.74 RPM	173.78 RPM
SRP021940_cerebellum	58.58 RPM	191.16 RPM
SRP021940_embryo	121.16 RPM	169.44 RPM
SRP021940_placental_villous	113.06 RPM	198.46 RPM
SRP021940_synovial_membrane	58.94 RPM	114.42 RPM
SRP021940_testis	49.88 RPM	529.13 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_62 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_62 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_62 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_137
Sus scrofa	retro_sscr_93
Canis familiaris	retro_cfam_20

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010988	1 retrocopy	retro_btau_137,
Canis familiaris	ENSCAFG00000014113	1 retrocopy	retro_cfam_20,
Callithrix jacchus	ENSCJAG00000002214	5 retrocopies	retro_cjac_2113, retro_cjac_2280, retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Cavia porcellus	ENSCPOG00000003778	3 retrocopies	retro_cpor_114, retro_cpor_1409, retro_cpor_915,
Equus caballus	ENSECAG00000008091	1 retrocopy	retro_ecab_62 ,
Felis catus	ENSFCAG00000012197	1 retrocopy	retro_fcat_75,
Loxodonta africana	ENSLAFG00000009851	1 retrocopy	retro_lafr_62,
Myotis lucifugus	ENSMLUG00000001756	1 retrocopy	retro_mluc_324,
Monodelphis domestica	ENSMODG00000011517	2 retrocopies	retro_mdom_150, retro_mdom_158,
Oryctolagus cuniculus	ENSOCUG00000015117	2 retrocopies	retro_ocun_108, retro_ocun_21,
Otolemur garnettii	ENSOGAG00000006047	4 retrocopies	retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Sorex araneus	ENSSARG00000004519	1 retrocopy	retro_sara_15,
Sarcophilus harrisii	ENSSHAG00000018402	1 retrocopy	retro_shar_393,
Ictidomys tridecemlineatus	ENSSTOG00000013294	3 retrocopies	retro_itri_111, retro_itri_1545, retro_itri_1608,