RetrogeneDB ID: retro_cpor_1409

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:52866214..52867053(+)
• Located in intron of: ENSCPOG00000004751

Retrocopy information

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

Parental gene information

• Parental gene symbol: MORF4L1
• Ensembl ID: ENSCPOG00000003778
• Aliases: None
• Description: mortality factor 4 like 1 [Source:HGNC Symbol;Acc:16989]

Sequence

>retro_cpor_1409
ATACACTACAGTGAGTGGAATAAAAATTGGGATGAGTGGGTTCCAGAAAGCAGGGTACTCAAGTATGTGGACACCAATCT
GCAGAAACAGCGAGAACTTCAAAAGGCCAATCAGGAGCAATACCCAGAGGGAAAGATGAGAGGGGCTGCTCCAGGAAAGA
AGACAGCTGATCTGCAACAGAAGAATGTTGACGTGAAAACTAAAAAGAACAAACCAAAAACCCCTGGTAATGGAGATGGT
GGCAGTACCAGTGAGACACCTCAGCCTCCTCGGAAGAAGAGGGCCCGGGTAGATCCTACTGTTGAAAATGAAGAAACTTT
TATGAACAGAATTGAAGTTAAAGTAAAGATTCCTGAAGAGCTAAAACCGTGGCTTGTTGATGACTGGGACCTAATTACTA
GACAGAAACAGCTGTTTTATCTTCCTGCCAAGAAGAATGTGGATTCCATTCTAGAGGACTATGCAAATTACAAGAAATCT
CGTGGAAACACGGATAATAAGGAGTATGCAGTTAATGAGGTTGTAGCAGGGATTAAAGAATACTTCAATGTGATGCTGGG
CACTCAGCTCTTCTACAAATTTGAGAGACCACAGTATGCAGAGATCCTTGCTGATCACCCTGATGCACCCATGTCACAGG
TGTATGGAGCACCACATCTACTGAGATTATTTGTACTAATTGGAGCGATGTAGGCCTACACACCTCTGGATGAGAAAAGC
CTTGCTTTATTACTGAATTATCTTCATGACTTCCTCAAGTATCTGGCGAAGAATTCAGCAACCTTGTTTAGTGCCAGTGA
TTATGAAGTGGCCCCCCTGAGTACCATCGGAAAGCAGTG

Alignment

ORF - retro_cpor_1409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.31 %
• Parental protein coverage: 77.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VHHPLLTSSWDEWVPESRVLKYVDTNLQKQRELQKANQEQYAEGKMRGAAPGKKTAGLQQKNVDVKTKKN
          .H.......WDEWVPESRVLKYVDTNLQKQRELQKANQEQY.EGKMRGAAPGKKTA.LQQKNVDVKTKKN
Retrocopy IHYSEWNKNWDEWVPESRVLKYVDTNLQKQRELQKANQEQYPEGKMRGAAPGKKTADLQQKNVDVKTKKN

Parental  KQKTPGNGDGGSTSETPQPPRKKRARVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFY
          K.KTPGNGDGGSTSETPQPPRKKRARVDPTVENEETFMNR.EVKVKIPEELKPWLVDDWDLITRQKQLFY
Retrocopy KPKTPGNGDGGSTSETPQPPRKKRARVDPTVENEETFMNRIEVKVKIPEELKPWLVDDWDLITRQKQLFY

Parental  LPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAP
          LPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQL.YKFERPQYAEILADHPDAP
Retrocopy LPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLFYKFERPQYAEILADHPDAP

Parental  MSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVA-PPEYHRKA
          MSQVYGAPHLLRLFV.IGAM.AYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVA.PPEYHRKA
Retrocopy MSQVYGAPHLLRLFVLIGAM*AYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVA<PPEYHRKA

Parental  V
          V
Retrocopy V

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
SRP017611_brain	3.97 RPM	120.21 RPM
SRP017611_kidney	9.42 RPM	217.33 RPM
SRP017611_liver	4.57 RPM	104.03 RPM
SRP040447_lung	4.54 RPM	197.23 RPM
SRP040447_skeletal_muscle	3.00 RPM	132.71 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1409 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1409 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,