RetrogeneDB ID: retro_sscr_93

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:98343235..98344102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012534
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MORF4L1
• Ensembl ID: ENSSSCG00000001769
• Aliases: None
• Description: mortality factor 4 like 1 [Source:HGNC Symbol;Acc:16989]

Sequence

>retro_sscr_93
ATGAGTTCCAGAAAGCAGGGTTCTCAAACTCGTGGACAACAATCTGCAGAAGAAGACAACTTCAAAAAACCAACTAGAAG
CAATATGCAGAGAAGTAAGATGAGAGGAGCCTCCTCAGGAAAGAAGACCGCTGGTCCACAGCAGAAGAATCTGGAAGCAG
CACTCCCCGGCAGGTGGGGGGGTCGCTCTGCAGAGACCCCCCCTTCGGGGTCCGTGAGGAAGACCAGAAAGAACAAACAG
AAGACCCCTGGAAATGGAGATGGTGGCAGTACCAGCGAAGCACCTCAGCCACCTCGGAAGAAAAGGGCCCGGGCTGACCC
CACTGTGGAAAGTGAGGAGGCATTTAAGAATAGAATGGAAGTGAAAGTGAAGATTCCTGAAGAATTAAAACCATGGCTAG
TTGAGGACTGGGACTTAGTTACCAGGCAGAAGCAGCTCTTTCAACTCCCTGCTAAGAAAAATGTAGATGCCATTCTGGAA
GAGTACGCAAATTGCAAGAAATCACAGGGAAATGTTGATAATAAGGAGTATGCGGTTAATGAAGTTGTGGCAGGAATAAA
AGAGTATTTCAATGTGATGTTGGGCACTCAGCTGCTCTATAAATTTGAGAGGCCCCAGTATGCCGAAATCCTCTTGGCTC
ACCCTGATGCGCCCATGTCCCAGGTTTATGGGGCACCACACCTACTGAGATTATTTGTGAGAATTGGAGCAATGTTGGCA
TATACGCCCCTTGATGAGAAGAGCCTTGCATTATTGTTGGGCTATCTGCATGATTTCCTAAAATACCTGGCAAAGAATGC
TGCGTCTCTGTTTACTGCCAGTGATTATAAAGTGGCTTCTGCTGAGTACCACCGCAAAGCCCTGTGA

Alignment

ORF - retro_sscr_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.84 %
• Parental protein coverage: 75.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGEGGSTSETPQPPRKKRARVDPTVENEETF
          Q....E....G...G..........V..KT.KNKQKTPGNG.GGSTSE.PQPPRKKRAR.DPTVE.EE.F
Retrocopy QQKNLEAALPGRWGGRSAETPPSGSVR-KTRKNKQKTPGNGDGGSTSEAPQPPRKKRARADPTVESEEAF

Parental  MNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAG
          .NR.EVKVKIPEELKPWLV.DWDL.TRQKQLF.LPAKKNVD.ILE.YAN.KKS.GN.DNKEYAVNEVVAG
Retrocopy KNRMEVKVKIPEELKPWLVEDWDLVTRQKQLFQLPAKKNVDAILEEYANCKKSQGNVDNKEYAVNEVVAG

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
SRP014902_placenta	61.19 RPM	76.45 RPM
SRP014902_testis	75.39 RPM	163.23 RPM
SRP018288_heart	84.50 RPM	221.73 RPM
SRP018288_kidney	182.24 RPM	264.49 RPM
SRP018288_liver	204.52 RPM	168.07 RPM
SRP018288_lung	59.36 RPM	188.89 RPM
SRP018856_adipose	61.58 RPM	373.82 RPM
SRP035408_brain	317.38 RPM	301.95 RPM
SRP035408_liver	425.13 RPM	249.94 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_93 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_93 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_93 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_137
Canis familiaris	retro_cfam_20
Equus caballus	retro_ecab_62

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012344	1 retrocopy	retro_amel_124,
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,
Homo sapiens	ENSG00000185787	3 retrocopies	retro_hsap_309, retro_hsap_3125, retro_hsap_850,
Gorilla gorilla	ENSGGOG00000016826	3 retrocopies	retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana	ENSLAFG00000009851	1 retrocopy	retro_lafr_62,
Macaca mulatta	ENSMMUG00000022926	1 retrocopy	retro_mmul_1064,
Monodelphis domestica	ENSMODG00000011517	2 retrocopies	retro_mdom_150, retro_mdom_158,
Mustela putorius furo	ENSMPUG00000015429	1 retrocopy	retro_mputfur_180,
Mus musculus	ENSMUSG00000062270	9 retrocopies	retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys	ENSNLEG00000008678	3 retrocopies	retro_nleu_417, retro_nleu_445, retro_nleu_51,
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,
Pongo abelii	ENSPPYG00000006703	4 retrocopies	retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes	ENSPTRG00000007351	3 retrocopies	retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus	ENSRNOG00000014410	6 retrocopies	retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sarcophilus harrisii	ENSSHAG00000018402	1 retrocopy	retro_shar_393,
Sus scrofa	ENSSSCG00000001769	1 retrocopy	retro_sscr_93 ,
Ictidomys tridecemlineatus	ENSSTOG00000013294	3 retrocopies	retro_itri_111, retro_itri_1545, retro_itri_1608,